There isn’t any reason why you can’t do both. I’ve technically been enrolled as a postgraduate student whilst completing all three of my MCSE certifications, but I really don’t want to get into the saga that is the writing of my Ph.D thesis.

What each option will bring to your career is very different.

A Masters degree is going to be more useful to you if you are headed towards management than a certification such as an MCSE or MCSA would be. If you’ve been a sysadmin for some time and are starting to think about moving towards management in future, heading towards university makes sense.

An MCSA or MCSE is going to be more immediately useful to you if you see yourself working more directly with technology in the immediate future. If your planning to still be a systems administrator in five or ten years time, you’d be better served keeping current with your technology certifications. The graduate degree can wait.